Baldonado spent the following year with the Single-A Savannah Sand Gnats, working to an excellent 1.91 ERA with 74 strikeouts in 56.2 innings pitched across 38 appearances.

In 2017, Baldonado played for the Double-A Binghamton Rumble Ponies and the Triple-A Las Vegas 51s, accumulating a 4.80 ERA in 50 appearances between the two affiliates.

[2] He spent the season with the Triple-A Iowa Cubs and was named a Pacific Coast League All-Star after pitching to a 4.88 ERA in 37 games.

[4] On June 16, 2019, Baldonado latched on with the High Point Rockers of the independent Atlantic League of Professional Baseball, for whom he pitched in 13 games, recording a 1.98 ERA with 19 strikeouts in 13 contests.

After putting up a 2.88 ERA across the two levels, Baldonado had his contract selected September 1, and was promoted to the major leagues for the first time.

[9][10] Baldonado made his major league debut against the Philadelphia Phillies on September 2, pitching a scoreless inning of relief.